Download Strategy for adding GO to large data sets

Adding GO for Large
Datasets
COST Functional Modeling Workshop
22-24 April, Helsinki
Large Datasets
RNASeq data sets and etc.:
 large data sets
 often there is little functional information
available
 many enrichment analysis tools will not
accept large gene lists
 RNASeq data sets also contain “novel”
genes
1. Finding Existing GO
1. Use GOProfiler to search based upon taxon or
name.
2. Check the GO Consortium Website to see if
your species of interest has an active
annotation effort.
• or to determine which relate species may have GO
annotations that can be transferred
3. Use QuickGO or GOProfiler to download
existing GO annotations.
4. Add your own GO annotations…
download GO
annotation file
from this link
http://geneontology.org/
2. Adding High-throughput GO
nt fasta file
aa fasta file
EMBOSS Transeq
(or etc)
species’
taxon ID
GOanna/
Blast2GO,
etc
InterProScan
list of motifs
and domains
InterPro2GO
GO association
file (IEA, ND)
BLAST database
of EXP GO
annotations for
related species
Note: AgBase & iPlant are working to make
these tools freely available via the AgBase &
iPlant websites.
GO association
file (ISA)
combine to
make single
GO annotation
file
http://www.ebi.ac.uk/Tools/emboss
Comments
1. Translating transcripts to proteins:
• many different programs
• most assume proteins > 100aa
• assume that proteins is translated from longest ORF
• EMBOSS – free and high-throughput; also available on Galaxy,
iPlant
2. InterProScan:
• searches sequences for conserved domains and motifs
• very intensive computing (needs HPC)
• Online tools at EBI – limited to proteins, low throughput
• iPlant – is preparing an instance
• AgBase – can help
3. InterPro2GO
• Script that converts InterPro IDs into their corresponding GO IDs
• Available at geneontology.org
Comments
4. Adding GO using Blast:
• Need to identify related species that have experimental GO
• Search database of experimental GO (should not transfer
annotations with IEA, ISS, etc evidence codes)
• Use a test set of sequences to identify Blast parameters (e.g.
Evalues, expect, etc.) for the full dataset
5. Combining GO from InterProScan & Blast:
• Remove any duplicate annotations derived from InterProScan (IEA)
and Blast (ISA).
• Remove any “no data” (ND) annotations where you have added an
annotation using Blast.
Note: GO IEA annotations are continually updated (by
manual review) and are considered out of date after
one year.
For help with adding GO, contact AgBase.